Title: Examples using 'Rcpp' to Interface R and C++
Description: Examples for Seamless R and C++ integration
The 'Rcpp' package contains a C++ library that facilitates the integration of
R and C++ in various ways. This package provides some usage examples.
Note that the documentation in this package currently does not cover all the
features in the package. The site <http://gallery.rcpp.org> regroups a large
number of examples for 'Rcpp'.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppExamples versions 0.1.8 dated 2016-11-24 and 0.1.9 dated 2019-08-24
ChangeLog | 55 +++++++++++++++++++++++++ DESCRIPTION | 18 +++----- MD5 | 26 ++++++------ NAMESPACE | 18 ++++---- R/RcppDataFrame.R | 4 - R/RcppExports.R | 16 +++---- README.md | 2 inst/NEWS.Rd | 20 +++++++-- man/RcppStringVectorExample.Rd | 2 src/DateExample.cpp | 27 ++++++------ src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 88 ++++++++++++++++++++++++----------------- src/StringVectorExample.cpp | 7 ++- 14 files changed, 188 insertions(+), 99 deletions(-)
Title: Simulation-Based Inference Methods for Infectious Disease Models
Description: Provides some code to run simulations of state-space models, and then
use these in the Approximate Bayesian Computation Sequential Monte Carlo (ABC-SMC)
algorithm of Toni et al. (2009) <doi:10.1098/rsif.2008.0172> and a bootstrap particle
filter based particle Markov chain Monte Carlo (PMCMC) algorithm
(Andrieu et al., 2010 <doi:10.1111/j.1467-9868.2009.00736.x>).
Also provides functions to plot and summarise the outputs.
Author: Trevelyan J. McKinley [aut, cre],
Stefan Widgren [aut] (Author of 'R/mparse.R'),
Pavol Bauer [cph] (R/mparse.R),
Robin Eriksson [cph] (R/mparse.R),
Stefan Engblom [cph] (R/mparse.R)
Maintainer: Trevelyan J. McKinley <t.mckinley@exeter.ac.uk>
Diff between SimBIID versions 0.1.0 dated 2019-08-23 and 0.1.1 dated 2019-08-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 ++++++- src/bootstrapParticleFilter.cpp | 2 +- src/bootstrapParticleFilterState.cpp | 15 +++++++++++---- tests/testthat/PMCMCpred | 24 ++++++++++++------------ 6 files changed, 38 insertions(+), 26 deletions(-)
Title: Simulations of Matrix Variate Distributions
Description: Provides samplers for various matrix variate distributions: Wishart, inverse-Wishart, normal, t, inverted-t, Beta type I, Beta type II, Gamma, confluent hypergeometric. Allows to simulate the noncentral Wishart distribution without the integer restriction on the degrees of freedom.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between matrixsampling versions 1.1.0 dated 2018-02-21 and 2.0.0 dated 2019-08-24
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++++++------ NAMESPACE | 4 ++++ NEWS.md | 6 +++++- R/CHIIkindtwo.R |only R/CHIkindtwo.R |only R/CHkindone.R |only R/gamma.R |only R/internal.R | 6 ++++++ README.md | 2 +- man/rmatrixCHIIkind2.Rd |only man/rmatrixCHIkind2.Rd |only man/rmatrixCHkind1.Rd |only man/rmatrixgamma.Rd |only man/rwishart.Rd | 3 ++- 15 files changed, 39 insertions(+), 16 deletions(-)
More information about matrixsampling at CRAN
Permanent link
Title: An Implementation of Isolation Forest
Description: Isolation forest is anomaly detection method introduced by the paper Isolation based Anomaly Detection (Liu, Ting and Zhou <doi:10.1145/2133360.2133363>).
Author: Komala Sheshachala Srikanth [aut, cre]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>
Diff between solitude versions 0.1.3 dated 2019-06-05 and 0.2.0 dated 2019-08-24
solitude-0.1.3/solitude/R/fastDoCall.R |only solitude-0.1.3/solitude/R/isolation_forest.R |only solitude-0.1.3/solitude/R/predict.R |only solitude-0.1.3/solitude/man/anomaly_score.Rd |only solitude-0.1.3/solitude/man/average_path_length.Rd |only solitude-0.1.3/solitude/man/compute_anomaly.Rd |only solitude-0.1.3/solitude/man/depth_corrected.Rd |only solitude-0.1.3/solitude/man/depth_terminalNodes.Rd |only solitude-0.1.3/solitude/man/fastDoCall.Rd |only solitude-0.1.3/solitude/man/harmonic.Rd |only solitude-0.1.3/solitude/man/harmonic_approx.Rd |only solitude-0.1.3/solitude/man/harmonic_exact.Rd |only solitude-0.1.3/solitude/man/predict.solitude.Rd |only solitude-0.2.0/solitude/DESCRIPTION | 13 - solitude-0.2.0/solitude/MD5 | 33 +--- solitude-0.2.0/solitude/NAMESPACE | 4 solitude-0.2.0/solitude/NEWS.md | 5 solitude-0.2.0/solitude/R/isolationForest_r6.R |only solitude-0.2.0/solitude/R/package_solitude.R | 7 solitude-0.2.0/solitude/R/terminal_nodes.R |only solitude-0.2.0/solitude/R/utils.R |only solitude-0.2.0/solitude/README.md | 106 +++++++++------ solitude-0.2.0/solitude/man/is_integerish.Rd |only solitude-0.2.0/solitude/man/isolationForest.Rd | 90 +++++++++--- solitude-0.2.0/solitude/man/solitude.Rd | 2 solitude-0.2.0/solitude/man/terminalNodesDepth.Rd |only solitude-0.2.0/solitude/man/terminalNodesDepthPerTree.Rd |only 27 files changed, 171 insertions(+), 89 deletions(-)
Title: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Description: General purpose TIFF file I/O for R users.
Currently the only such package with read and write support for TIFF
files with floating point (real-numbered) pixels, and the only package
that can correctly import TIFF files that were saved from 'ImageJ' and
write TIFF files than can be correctly read by 'ImageJ'
<https://imagej.nih.gov/ij/>. Also supports text image I/O.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>),
Kent Johnson [aut],
Simon Urbanek [ctb],
Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>),
Jeroen Ooms [rev, ctb] (<https://orcid.org/0000-0002-4035-0289>),
Jon Clayden [rev] (<https://orcid.org/0000-0002-6608-0619>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between ijtiff versions 2.0.2 dated 2019-07-06 and 2.0.3 dated 2019-08-24
DESCRIPTION | 82 ++++++++++++++++++------------- MD5 | 12 ++-- NEWS.md | 6 ++ build/vignette.rds |binary inst/doc/reading-and-writing-images.html | 18 ++++-- inst/doc/text-images.html | 8 ++- inst/doc/the-imagej-problem.html | 10 ++- 7 files changed, 84 insertions(+), 52 deletions(-)
Title: Hierarchical Bayesian ANOVA Models
Description: It covers several Bayesian Analysis of Variance (BANOVA) models used in analysis of experimental designs in which both within- and between- subjects factors are manipulated. They can be applied to data that are common in the behavioral and social sciences. The package includes: Hierarchical Bayes ANOVA models with normal response, t response, Binomial (Bernoulli) response, Poisson response, ordered multinomial response and multinomial response variables. All models accommodate unobserved heterogeneity by including a normal distribution of the parameters across individuals. Outputs of the package include tables of sums of squares, effect sizes and p-values, and tables of predictions, which are easily interpretable for behavioral and social researchers. The floodlight analysis and mediation analysis based on these models are also provided. BANOVA uses 'Stan' and 'JAGS' as the computational platform.
Author: Chen Dong, Michel Wedel
Maintainer: Chen Dong <cdong@math.umd.edu>
Diff between BANOVA versions 1.1.3 dated 2019-07-21 and 1.1.4 dated 2019-08-24
DESCRIPTION | 10 +++++----- MD5 | 42 +++++++++++++++++++++--------------------- NEWS | 4 ++++ inst/doc/banova_examples.R | 2 ++ inst/doc/banova_examples.Rmd | 2 ++ inst/doc/banova_examples.html | 6 ++++-- man/BANOVA-package.Rd | 4 ++-- man/BANOVA.floodlight.Rd | 1 + man/BANOVA.mediation.Rd | 1 + man/BANOVA.run.Rd | 1 + man/BAnova.Rd | 1 + man/bpndata.Rd | 1 + man/colorad.Rd | 1 + man/colorad2.Rd | 1 + man/condstudy.Rd | 1 + man/conv.diag.Rd | 1 + man/goalstudy.Rd | 2 +- man/pairs.BANOVA.Rd | 1 + man/table.predictions.Rd | 1 + man/table.pvalues.Rd | 1 + man/trace.plot.Rd | 1 + vignettes/banova_examples.Rmd | 2 ++ 22 files changed, 56 insertions(+), 31 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects and unknown variance-covariance structures (i.e. heterogeneous and unstructured variance models) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) and dense known covariance structures for levels of random effects. Spatial models can also be fitted using i.e. the two-dimensional spline functionality available in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.0.1 dated 2019-07-02 and 4.0.4 dated 2019-08-24
DESCRIPTION | 8 MD5 | 152 ++++++------ R/FUN_stats.R | 2 R/FUN_utils.R | 433 +++++++++++++++++++----------------- R/GWAS.R | 4 R/mmer.R | 109 ++++----- data/DT_augment.RData |binary data/DT_btdata.RData |binary data/DT_cornhybrids.RData |binary data/DT_cpdata.RData |binary data/DT_example.RData |binary data/DT_expdesigns.RData |binary data/DT_fulldiallel.RData |binary data/DT_gryphon.RData |binary data/DT_h2.RData |binary data/DT_halfdiallel.RData |binary data/DT_legendre.RData |binary data/DT_polyploid.RData |binary data/DT_rice.RData |binary data/DT_technow.RData |binary data/DT_wheat.RData |binary data/DT_yatesoats.RData |binary data/datalist | 31 +- inst/doc/sommer.FAQ.R | 15 + inst/doc/sommer.FAQ.Rmd | 17 + inst/doc/sommer.FAQ.pdf |binary inst/doc/sommer.R | 50 +++- inst/doc/sommer.Rmd | 50 +++- inst/doc/sommer.changes.pdf |binary inst/doc/sommer.pdf |binary inst/doc/sommer.start.R | 23 + inst/doc/sommer.start.Rmd | 23 + inst/doc/sommer.start.pdf |binary man/DT_augment.Rd | 6 man/DT_btdata.Rd | 2 man/DT_cornhybrids.Rd | 9 man/DT_cpdata.Rd | 5 man/DT_example.Rd | 3 man/DT_expdesigns.Rd | 1 man/DT_fulldiallel.Rd | 2 man/DT_gryphon.Rd | 6 man/DT_h2.Rd | 1 man/DT_halfdiallel.Rd | 1 man/DT_legendre.Rd | 1 man/DT_polyploid.Rd | 6 man/DT_rice.Rd | 7 man/DT_technow.Rd | 9 man/DT_wheat.Rd | 3 man/DT_yatesoats.Rd | 1 man/EMMA.Rd | 11 man/GWAS.Rd | 6 man/at.Rd | 6 man/atcg1234.Rd | 4 man/bivariateRun.Rd | 3 man/build.HMM.Rd | 6 man/cs.Rd | 4 man/ds.Rd | 4 man/fcm.Rd | 3 man/fill.design.Rd | 1 man/h2.fun.Rd | 2 man/leg.Rd | 6 man/mmer.Rd | 8 man/overlay.Rd | 1 man/pin.Rd | 51 ++-- man/sommer-package.Rd | 1 man/spatPlots.Rd | 5 man/spl2D.Rd | 5 man/us.Rd | 4 man/vs.Rd | 8 src/MNR.cpp | 33 +- vignettes/sommer.FAQ.Rmd | 17 + vignettes/sommer.FAQ.html | 97 ++++---- vignettes/sommer.Rmd | 50 +++- vignettes/sommer.changes.html | 4 vignettes/sommer.html | 492 ++++++++++++++++++++++-------------------- vignettes/sommer.start.Rmd | 23 + vignettes/sommer.start.html | 273 ++++++++++++----------- 77 files changed, 1239 insertions(+), 869 deletions(-)
Title: Create a Random List for Crossover Studies
Description: Contains a function to randomize subjects, patients in groups of
sequences (treatment sequences).
If a blocksize is given, the randomization will be done within blocks.
The randomization may be controlled by a Wald-Wolfowitz runs test.
Functions to obtain the p-value of that test are included.
The package is mainly intended for randomization of bioequivalence studies
but may be used also for other clinical crossover studies.
Contains two helper functions sequences() and williams() to get the sequences
of commonly used designs in BE studies.
Author: D. Labes
Maintainer: D. Labes <detlewlabes@gmx.de>
Diff between randomizeBE versions 0.3-4 dated 2018-06-20 and 0.3-5 dated 2019-08-24
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS | 10 +++++----- R/sequences.R | 3 ++- man/randomizeBE-package.Rd |only 5 files changed, 15 insertions(+), 13 deletions(-)
Title: Bound Constrained Optimal Sample Allocation
Description: Implements bound constrained optimal sample allocation (BCOSA) framework described in Bulus & Dong (2019) <doi:10.1080/00220973.2019.1636197> for power analysis of multilevel regression discontinuity designs (MRDDs) and multilevel randomized trials (MRTs) with continuous outcomes. Separate tools for statistical power and minimum detectable effect size computations are provided.
Author: Metin Bulus [aut, cre],
Nianbo Dong [aut]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Diff between cosa versions 1.2.2 dated 2019-05-09 and 2.0.0 dated 2019-08-24
cosa-1.2.2/cosa/R/method.R |only cosa-1.2.2/cosa/R/plot.R |only cosa-1.2.2/cosa/man/plot.Rd |only cosa-2.0.0/cosa/DESCRIPTION | 12 cosa-2.0.0/cosa/MD5 | 81 +-- cosa-2.0.0/cosa/NAMESPACE | 29 + cosa-2.0.0/cosa/NEWS.md | 9 cosa-2.0.0/cosa/R/bcrd3f2.R | 288 +++++++----- cosa-2.0.0/cosa/R/bcrd3r2.R | 264 ++++++----- cosa-2.0.0/cosa/R/bcrd4f3.R | 292 +++++++------ cosa-2.0.0/cosa/R/bcrd4r2.R | 255 ++++++----- cosa-2.0.0/cosa/R/bcrd4r3.R | 268 +++++++----- cosa-2.0.0/cosa/R/bird2f1.R | 321 +++++++------- cosa-2.0.0/cosa/R/bird2r1.R | 281 +++++++----- cosa-2.0.0/cosa/R/bird3r1.R | 287 +++++++----- cosa-2.0.0/cosa/R/bird4r1.R | 265 +++++++---- cosa-2.0.0/cosa/R/crd2r2.R | 287 +++++++----- cosa-2.0.0/cosa/R/crd3r3.R | 286 +++++++----- cosa-2.0.0/cosa/R/crd4r4.R | 282 +++++++----- cosa-2.0.0/cosa/R/errors.R |only cosa-2.0.0/cosa/R/ird1r1.R | 209 ++++----- cosa-2.0.0/cosa/R/methods.R |only cosa-2.0.0/cosa/R/moments.R |only cosa-2.0.0/cosa/R/plots.R |only cosa-2.0.0/cosa/R/utils.R | 144 ++---- cosa-2.0.0/cosa/README.md | 57 +- cosa-2.0.0/cosa/build/vignette.rds |binary cosa-2.0.0/cosa/inst/CITATION | 4 cosa-2.0.0/cosa/inst/doc/cosa_tutorial.R | 123 +++-- cosa-2.0.0/cosa/inst/doc/cosa_tutorial.Rmd | 128 +++-- cosa-2.0.0/cosa/inst/doc/cosa_tutorial.html | 623 +++++++++++++++++++++------- cosa-2.0.0/cosa/man/bcrd3r2.Rd | 110 ++-- cosa-2.0.0/cosa/man/bcrd4r2.Rd | 122 +++-- cosa-2.0.0/cosa/man/bcrd4r3.Rd | 117 ++--- cosa-2.0.0/cosa/man/bird2r1.Rd | 123 +++-- cosa-2.0.0/cosa/man/bird3r1.Rd | 135 +++--- cosa-2.0.0/cosa/man/bird4r1.Rd | 137 +++--- cosa-2.0.0/cosa/man/cosa-deprecated.Rd |only cosa-2.0.0/cosa/man/cosa-package.Rd | 4 cosa-2.0.0/cosa/man/crd2r2.Rd | 157 +++---- cosa-2.0.0/cosa/man/crd3r3.Rd | 160 ++++--- cosa-2.0.0/cosa/man/crd4r4.Rd | 124 ++--- cosa-2.0.0/cosa/man/inspect.Rd |only cosa-2.0.0/cosa/man/ird1r1.Rd | 116 +++-- cosa-2.0.0/cosa/man/moments.Rd |only cosa-2.0.0/cosa/man/plots.Rd |only cosa-2.0.0/cosa/vignettes/cosa_tutorial.Rmd | 128 +++-- 47 files changed, 3686 insertions(+), 2542 deletions(-)
Title: Class Unions, Matrix Operations, and Color Schemes for OOMPA
Description: Provides the class unions that must be
preloaded in order for the basic tools in the OOMPA (Object-Oriented
Microarray and Proteomics Analysis) project to be defined and loaded.
It also includes vectorized operations for row-by-row means,
variances, and t-tests. Finally, it provides new color schemes.
Details on the packages in the OOMPA project can be found at
<http://oompa.r-forge.r-project.org/>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between oompaBase versions 3.2.8 dated 2019-05-06 and 3.2.9 dated 2019-08-24
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 5 +++-- R/b02-colorSchemes.R | 10 ++++++++++ inst/doc/oompa.R | 18 +++++++++++------- inst/doc/oompa.Rnw | 8 +++++--- inst/doc/oompa.pdf |binary man/z02-colorSchemes.Rd | 3 +++ vignettes/oompa.Rnw | 8 +++++--- 9 files changed, 49 insertions(+), 27 deletions(-)
Title: Structural Crystallography in 1d
Description: Functions to carry out the most important crystallographic calculations for crystal
structures made of 1d Gaussian-shaped atoms, especially useful for methods development.
Main reference: E. Smith, G. Evans, J. Foadi (2017) <doi:10.1088/1361-6404/aa8188>.
Author: James Foadi [cre, aut]
Maintainer: James Foadi <j.foadi@bath.ac.uk>
Diff between crone versions 0.1.0 dated 2019-07-27 and 0.1.1 dated 2019-08-24
crone-0.1.0/crone/vignettes/BIBLIOGRAPHY.bib |only crone-0.1.1/crone/DESCRIPTION | 8 ++--- crone-0.1.1/crone/MD5 | 39 +++++++++++++-------------- crone-0.1.1/crone/NEWS.md | 5 ++- crone-0.1.1/crone/inst/doc/tutorial01.R | 3 -- crone-0.1.1/crone/inst/doc/tutorial01.Rnw | 18 +++++++----- crone-0.1.1/crone/inst/doc/tutorial01.pdf |binary crone-0.1.1/crone/inst/doc/tutorial02.pdf |binary crone-0.1.1/crone/inst/doc/tutorial03.R | 3 -- crone-0.1.1/crone/inst/doc/tutorial03.Rnw | 18 +++++++----- crone-0.1.1/crone/inst/doc/tutorial03.pdf |binary crone-0.1.1/crone/inst/doc/tutorial04.R | 3 -- crone-0.1.1/crone/inst/doc/tutorial04.Rnw | 31 ++++++++++++--------- crone-0.1.1/crone/inst/doc/tutorial04.pdf |binary crone-0.1.1/crone/inst/doc/tutorial05.R | 3 -- crone-0.1.1/crone/inst/doc/tutorial05.Rnw | 23 +++++++++------ crone-0.1.1/crone/inst/doc/tutorial05.pdf |binary crone-0.1.1/crone/vignettes/tutorial01.Rnw | 18 +++++++----- crone-0.1.1/crone/vignettes/tutorial03.Rnw | 18 +++++++----- crone-0.1.1/crone/vignettes/tutorial04.Rnw | 31 ++++++++++++--------- crone-0.1.1/crone/vignettes/tutorial05.Rnw | 23 +++++++++------ 21 files changed, 135 insertions(+), 109 deletions(-)
More information about statsExpressions at CRAN
Permanent link
More information about AzureVMmetadata at CRAN
Permanent link
Title: R Utilities Accompanying the Software Package BayesX
Description: Functions for exploring and visualising estimation results
obtained with BayesX, a free software for estimating structured additive
regression models (<http://www.BayesX.org>). In addition,
functions that allow to read, write and manipulate map objects that are required in spatial
analyses performed with BayesX.
Author: Nikolaus Umlauf [aut, cre],
Thomas Kneib [aut],
Nadja Klein [aut],
Felix Heinzl [ctb],
Andreas Brezger [ctb],
Daniel Sabanes Bove [ctb]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between BayesX versions 0.3-0 dated 2018-05-18 and 0.3-1 dated 2019-08-24
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/drawmap.R | 9 +++++---- man/BayesX-package.Rd | 12 ++++++++---- man/fuse.Rd | 4 ++-- 5 files changed, 23 insertions(+), 18 deletions(-)
Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Baltagi (2011) <doi:10.1007/978-3-642-20059-5> for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>
Diff between dLagM versions 1.0.15 dated 2019-07-18 and 1.0.17 dated 2019-08-24
DESCRIPTION | 13 +- MD5 | 32 +++--- NAMESPACE | 5 + NEWS.md | 11 +- R/ardlBound.R | 225 ++++++++++++++++++++++++++++++++++++++++++------- R/ardlBoundOrders.R | 74 +--------------- R/rolCorplot.R |only R/sdPercentiles.R |only build/partial.rdb |binary data/wheat.RData |binary man/ardlBound.Rd | 31 ++++-- man/ardlBoundOrders.Rd | 2 man/dLagM-package.Rd | 4 man/forecast.Rd | 2 man/koyckDlm.Rd | 9 + man/rolCorPlot.Rd |only man/sdPercentiles.Rd |only man/warming.Rd | 4 man/wheat.Rd | 2 19 files changed, 274 insertions(+), 140 deletions(-)
Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations,
weight-enabled frequency tables and common univariate
statistics in concise tables available in a variety of
formats (plain ASCII, Markdown and HTML). A good
point-of-entry for exploring data, both for experienced
and new R users.
Author: Dominic Comtois [aut, cre]
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 0.9.3 dated 2019-04-11 and 0.9.4 dated 2019-08-24
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Title: Deciphering Biological Networks with Patterned Heterogeneous
Measurements
Description: A modeling tool dedicated to biological network modeling. It allows for single or joint modeling of, for instance, genes and proteins. It starts with the selection of the actors that will be the used in the reverse engineering upcoming step. An actor can be included in that selection based on its differential measurement (for instance gene expression or protein abundance) or on its time course profile. Wrappers for actors clustering functions and cluster analysis are provided. It also allows reverse engineering of biological networks taking into account the observed time course patterns of the actors. Many inference functions are provided and dedicated to get specific features for the inferred network such as sparsity, robust links, high confidence links or stable through resampling links. Some simulation and prediction tools are also available for cascade networks. Example of use with microarray or RNA-Seq data are provided.
Author: Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>),
Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>)
Maintainer: Frederic Bertrand <frederic.bertrand@math.unistra.fr>
Diff between Patterns versions 1.0 dated 2019-06-07 and 1.1 dated 2019-08-24
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Title: Selection, Reverse-Engineering and Prediction in Cascade
Networks
Description: A modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Author: Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>),
Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>),
Laurent Vallat [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@math.unistra.fr>
Diff between Cascade versions 1.7 dated 2019-02-18 and 1.8 dated 2019-08-24
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